Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100653
Name   oriT_pXF51ud in_silico
Organism   Xylella fastidiosa strain U24d
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NZ_CP009791 (39537..39578 [+], 42 nt)
oriT length   42 nt
IRs (inverted repeats)      6..11, 12..17  (GGTTTT..AAAACC)
Location of nic site      24..25
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 42 nt

>oriT_pXF51ud
ATAGCGGTTTTAAAACCTATCCTGCCCTAGATTTAACCCTCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   725 GenBank   WP_010895239
Name   Nickase_pXF51ud insolico UniProt ID   _
Length   463 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 463 a.a.        Molecular weight: 52664.98 Da        Isoelectric Point: 10.8467

>WP_010895239.1 relaxase/mobilization nuclease domain-containing protein [Xylella fastidiosa]
MAGRLMGIIEAELGSALSPAVKRKVNNTKKLRSTAKRVTGRSSEVMVKVTGFGKGAGHVKAHLDYITRNG
KLEMENDRGEIFNGKEEVKEFFKDWEKDFGDGKRHKNQRDTMHMVLSMPETTDSESVKKSVREFAKATFG
KNHEYVFVLHTDEPHPHCHLTVKCLGFDGIRLNPRKADLHQWREGFAEKLRDQGVEAEATPRRSRGVVKK
AEPNVIRHIERGDKTHEPRVSKVKAAKVKEAAMELVAESKGLPVPPKPWEEAIKARQREIRRAWLTVAAE
LERENTRKTFNQKEARNDRPNYERISAEQARPAQRAASVYQSNLTKAGRQAPSRTVSSLRNVSCLGVVQH
RSSSKMLLQPNAPDRMGRNGRPNSEMRRSGTSNNGVDRDAKMLLDVYKPIEQNKVLAWRIRSFVEAMPSI
ETERHQIKRDLAQRFTKQAEKIHRKTNGQEQTGPKRGGKDVER

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(58-208)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 435..13189

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
XFUD_RS12940 (XFUD_12155) 47..301 + 255 WP_042464021 helix-turn-helix transcriptional regulator -
XFUD_RS12945 (XFUD_12160) 435..1010 + 576 WP_010895199 lytic transglycosylase domain-containing protein virB1
XFUD_RS12950 (XFUD_12165) 1012..2994 + 1983 WP_010895200 type I DNA topoisomerase -
XFUD_RS12955 (XFUD_12170) 3065..3328 + 264 WP_010895201 hypothetical protein -
XFUD_RS12960 (XFUD_12175) 3353..3709 + 357 WP_069106970 TrbC/VirB2 family protein virB2
XFUD_RS12965 (XFUD_12180) 3712..4080 + 369 WP_010895203 type IV secretion system protein VirB3 virB3
XFUD_RS12970 (XFUD_12185) 4094..6541 + 2448 WP_010895204 VirB4 family type IV secretion system protein virb4
XFUD_RS12975 (XFUD_12190) 6538..7218 + 681 WP_010895205 P-type DNA transfer protein VirB5 virB5
XFUD_RS12985 (XFUD_12200) 7551..7790 + 240 WP_143707257 hypothetical protein -
XFUD_RS12990 (XFUD_12205) 7794..8840 + 1047 WP_010895208 type IV secretion system protein virB6
XFUD_RS13000 (XFUD_12210) 9150..9971 + 822 WP_010895209 virB8 family protein virB8
XFUD_RS13005 (XFUD_12215) 9982..10818 + 837 WP_010895210 P-type conjugative transfer protein VirB9 virB9
XFUD_RS13010 (XFUD_12220) 10818..12161 + 1344 WP_010895211 type IV secretion system protein VirB10 virB10
XFUD_RS13015 (XFUD_12225) 12158..13189 + 1032 WP_042464027 P-type DNA transfer ATPase VirB11 virB11
XFUD_RS13020 (XFUD_12230) 13155..15164 + 2010 WP_042464030 type IV secretory system conjugative DNA transfer family protein -
XFUD_RS13025 (XFUD_12235) 15175..17466 + 2292 WP_010895214 LPD7 domain-containing protein -
XFUD_RS13030 (XFUD_12240) 17463..17660 + 198 WP_042464033 hypothetical protein -
XFUD_RS13035 (XFUD_12245) 17657..17983 + 327 WP_010895215 hypothetical protein -

Host bacterium

ID   1113 GenBank   NZ_CP009791
Plasmid name   pXF51ud Incompatibility group   _
Plasmid size   51156 bp Coordinate of oriT [Strand]   39537..39578 [+]
Host baterium   Xylella fastidiosa strain U24d

Cargo genes

Drug resistance gene   -
Virulence gene   virulence factor
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -